Hi, I can help you with this. I am a wordpress expert, and I´m familiar with myCRED. I have used myCRED in a previous project.
I just finished creating a platform like freelancer, where users can hire other users online, and I used myCRED for giving points based on the activity. I had to integrate myCRED into the platform and I created my own extension for giving points per custom actions.
So I think I can help you. I think the best way would be to continue using your theme´s system, but connect it with myCRED, so all the points are stored in myCRED and we´ll use the theme only for triggering the accreditation.
This way the points will be stored only in one place, the theme will work, and myCRED will work. Let me know if you want to discuss it.